[Freesurfer] mri_vol2surf - MNI subject

Hi, If I have volume data in MNI subject space (produced using --tal option in mri_vol2vol), how do I project it onto the surface in the same subject space? There does not seem to be an equivalent tal option in mri_vol2surf. Thanks, Yigal ___ Frees

[Freesurfer] Subcortical Label

Hello,    I´d like to know if there is some way to create a ROI-label of a subcortical structure. If there is a way, please tell me how to do. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br

Re: [Freesurfer] Subcortical Label

sure, what format would you like the ROI in? On Thu, 8 Jan 2009, Kelly Silva wrote: Hello,    I´d like to know if there is some way to create a ROI-label of a subcortical structure. If there is a way, please tell me how to do. T

Res: [Freesurfer] Subcortical Label

Hi,   I need that the ROI appears like a label, for example, together with the parcelations of aparc.a2005s.stats/aparc.stats, becaus I have a program that reads the labels from aparc.stats.     Thanks, Kelly De: Bruce Fischl Para: Kelly S

Re: Res: [Freesurfer] Subcortical Label

sorry, you mean in our .label format? I'm still not sure I understand. On Thu, 8 Jan 2009, Kelly Silva wrote: Hi,   I need that the ROI appears like a label, for example, together with the parcelations of aparc.a2005s.stats/aparc.stats, becaus I have a program that reads the labels from aparc

Re: [Freesurfer] Subcortical Label

Try mri_cor2label (name is not very descriptive) doug Kelly Silva wrote: Hello, I´d like to know if there is some way to create a ROI-label of a subcortical structure. If there is a way, please tell me how to do. Thanks, Kel

Res: Res: [Freesurfer] Subcortical Label

1) I need the command line to visualize the segmentation of subcortical structures, because I want to see if the segmentation of thalamus is good. 2) If the segmentation is not good, how can I make changes manually? 3) After the changes, is it necessary to run Recon2 and Recon3 again???   

Re: Res: Res: [Freesurfer] Subcortical Label

1) tkmedit $subject norm.mgz -segmentation aseg.mgz 2) there are editing tools in tkmedit you can use. 3) you'll need to regenerate the aseg.stats file and the aparc+aseg stuff, but if the edits aren't near cortex you don't necessarily have to. Unless you are really trying to save computer

Res: Res: Res: [Freesurfer] Subcortical Label

Thanks a lot! De: Bruce Fischl Para: Kelly Silva Cc: freesurfer@nmr.mgh.harvard.edu Enviadas: Quinta-feira, 8 de Janeiro de 2009 16:07:41 Assunto: Re: Res: Res: [Freesurfer] Subcortical Label 1) tkmedit $subject norm.mgz -segmentation aseg.mgz 2) there are

[Freesurfer] File cnr.mgh

Dear FS experts I am not sure whether the file cnr.mgh represents the contrast-to-noise ration (CNR) on one hand and how to interpret it. When I loaded the cnr.mgh in tkmedit, there is actually no image visible and only one value is shown e.g., 0.355 or -0.965. What do these values mean? In my op

Re: [Freesurfer] File cnr.mgh

you can use the binary mri_cnr to compute the CNR across a surface boundary (usually gray/white). What directory did you find the cnr.mgh file? cheers, Bruce On Thu, 8 Jan 2009, Jürgen Hänggi wrote: Dear FS experts I am not sure whether the file cnr.mgh represents the contrast-to-noise r

[Freesurfer] Problem running tksurfer

tksurfer fsaverage lh inflated surfer: current subjects dir: /autofs/space/ventzl_001/users/SUBJECTS_DIR surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/schnook_001/users/yigal/projects/functional surfer: Readin

[Freesurfer] Top Quartile of Active Voxels

Hello, I ran the following analysis to target task-specific voxels at a certain contrast and offset. func2roi-sess -roidef dACC10_lh -analysis EMerror -anatlabel dACC-lh -maskcontrast ASevfix -maskframe 5 -maskthresh 1 -masktail pos -maskmap sig -sf Subject_files/MTHFRn18-list -d $SUBJECTS_DIR I

Re: [Freesurfer] Top Quartile of Active Voxels

Sorry, I don't have anything that will do that. You could probably do it in matlab, if you know how to program in matlab. doug Dave Brohawn wrote: Hello, I ran the following analysis to target task-specific voxels at a certain contrast and offset. func2roi-sess -roidef dACC10_lh -analysis

[Freesurfer] Qdec correlation analyses

Hello, freesurfer group, I have run qdec for comparing thickness between two groups. When qdec does a correlation analyses for thickness versus a second variable: 1) Does the second variable have to be a continuous interval variable or 2) can the second variable be an ordinal variable with mor

Re: [Freesurfer] Qdec correlation analyses

It has to be interpreted as a continuous variable. The test is done using a t-test inside the glm. This reduces to a Pearson if there is only one variable and no intercept (which it is not). doug Xie, Hong wrote: Hello, freesurfer group, I have run qdec for comparing thickness betwee

Re: [Freesurfer] Top Quartile of Active Voxels

On Thursday 08 January 2009 15:29:47 Dave Brohawn wrote: > I would like to create a functional constraint including only the 25% > most active voxels (top quartile). > > Is there a command that can achieve this? > You can use 'mris_calc' (the development version): $>mris_calc someVolume.mgz stat

[Freesurfer] Can freesurfer flatten (and dsiplay) certain subcortical areas?

Can freesurfer flatten (and only display) a (or several) segmented subcortical area(s), e.g. hippocampal region? If yes, can the fine structures in such a region (such as CA1,2,3, DG, etc.) be labeled? Thanks, Mingwu ___ Freesurfer mailing list Free

[Freesurfer] Single subject statistical analysis

Dear FS statistical experts We would like to compared a single subject against a group using FS statistical machinery. There is a paper by Salat et al., Hippocampus, 2006, in which the amnestic patient H.M. was compared against 4 control subjects. How valid is such a statistical test in FS? Does